Biology subjects

Vu, Q.

Publications and source records attributed to Vu, Q..

4 recordsLinked to original sources

bioRxiv2026

Multidimensional encoding of temporal features underlies song recognition in Floridian Ormia ochracea

Acoustic communication signals often contain complex temporal structure, yet the features underlying signal recognition remain poorly understood, particularly in eavesdropping receivers. The parasitoid fly Ormia ochracea localises host crickets by eavesdropping on their calling songs. In Florida, preferred host songs consist of sound pulses repeated at ~50 pulses/s, and flies exhibit matching preferences. However, it remains unclear whether this preference reflects sensitivity to individual temporal features (e.g., pulse duration, interpulse interval) or to derived temporal relationships (e.g., pulse rate, pulse period, duty cycle) that emerge from their combination. We independently varied pulse duration and interpulse interval across a broad stimulus space and quantified tethered-walking phonotaxis using a switch-following paradigm. Behavioural responses formed a structured tuning surface, with high performance along a diagonal corresponding to 50 pulses/s, as well as elevated responses for a restricted range of pulse durations across a wide range of interpulse intervals. Responses failed to collapse across stimuli sharing the same pulse rate or pulse period, indicating that these features alone do not determine recognition. Instead, behaviour was best explained by the interacting effects of pulse duration and interpulse interval. These results demonstrate that song recognition in O. ochracea is multidimensional, with pulse rate tuning emerging from an underlying feature space rather than a single encoded parameter.

animal behavior and cognition↗

bioRxiv2026

AlphaFold Database expands to proteome-scale quaternary structures

Protein function is governed by molecular interactions, yet structural coverage of these interactions remains sparse. The AlphaFold Protein Structure Database (AFDB) transformed access to accurate monomeric protein structures at scale. Here, we expand the AFDB to quaternary structures by predicting 31M candidate homo- and heterodimeric protein complexes, compiled from 4,777 proteomes, including model- and global health organisms. We established confidence criteria via analysis of experimentally determined structures, resulting in 1.81M high-confidence predictions. These models enabled the discovery of emergent structures and topologies not present in monomeric predictions. Additionally, the top 1% of structural clusters accounted for [~]44% of all complexes, and [~]8.3% of clusters were conserved across multiple domains of life, pointing to a substantial fraction of ancient, universally retained assemblies. Structural search highlighted that high-confidence predictions are anchored in experimental multimer space, yet 31.3% extend beyond detectable PDB coverage. These freely accessible proteome-scale predictions facilitate functional and mechanistic hypothesis generation across biology.

synthetic biology↗

bioRxiv2025

A widespread protein misfolding mechanism is differentially rescued by chaperones based on gene essentiality

Protein misfolding involving changes in non-covalent lasso entanglement (NCLE) status has been proposed based on simulations and biochemical assays of a small number of proteins. Here, we detect hallmarks of these misfolded states across hundreds of proteins by integrating E. coli proteome-wide limited-proteolysis mass spectrometry with structural datasets of protein native structures. Proteins containing native NCLEs are twice as likely to misfold, predominantly in regions where these NCLEs naturally occur. Surprisingly, the chaperones DnaK and GroEL do not typically correct this misfolding, except in the case of essential proteins. Statistical analysis links this differential rescue activity to weaker loop-closing contacts in the NCLEs of essential proteins, suggesting misfolding involving these loops is easier to rectify by chaperones. Molecular simulations indicate a mechanism where premature NCLE loop closure, prior to proper placement of the threading segment, leads to persistent misfolded states. This mechanism explains why, in the mass spectrometry data, proteins with NCLEs are more likely to misfold and misfold in NCLE regions. These results suggest widespread NCLE misfolding, that such misfolded states in non-essential proteins can bypass the refolding action of chaperones, and that some protein sequences may have evolved to allow chaperone rescue from this class of misfolding.

biophysics↗

bioRxiv2024

Resource competition affects the developmental outcome of the acoustic parasitoid fly Ormia ochracea

Ormia ochracea is an acoustic parasitoid fly where the adults are free-living, but their larval young depend on nutritional resources within host crickets for growth and development. In nature, gravid female flies rely on their ability to recognize and localize cricket calling songs to find suitable host species to parasitize. In depth investigations of fly behavior and the mechanistic bases of auditory perception require a reliable approach to propagate stable fly colonies in the laboratory. Previous work has demonstrated that flies can be propagated using a number of natural host cricket species, as well as cricket species that flies do not parasitize in nature. However, we lack a complete understanding of fly developmental outcomes when non-host cricket species are utilized to propagate fly colonies. In this study, we document the feasibility of using commercially supplied Acheta domesticus as a host species. We specifically test the hypothesis that host size and resource competition can affect developmental outcomes of O. ochracea. We performed manual parasitizations on crickets that varied in size, and resource competition was varied by manipulating the number of larvae used to parasitize a host cricket. A series of morphometric analyses were conducted on host crickets, and developmental outcomes were measured in terms of pupation success and eclosion success, pupal width, and eclosed adult fly size. In the absence of resource competition, we found that host cricket size did not affect pupation or eclosion success. In the presence of resource competition between two developing larvae within a host cricket, pupation and eclosion successes were impacted negatively, and the developing pupae were more likely to be smaller. These results confirm that resource competition among developing parasitoids can negatively affect developmental outcomes, and Acheta domesticus can be used effectively to propagate colonies of O. ochracea in the laboratory. HighlightsO_LIThe acoustic parasitoid fly Ormia ochracea can successfully develop within the house cricket Acheta domesticus. C_LIO_LIPupal size and eclosed adult fly size varies positively with the size of host cricket. C_LIO_LIResource competition negatively affects pupation and eclosion success. C_LIO_LIResource competition resulted in smaller fly pupae that were less likely to eclose. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/590943v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@b86e19org.highwire.dtl.DTLVardef@44444corg.highwire.dtl.DTLVardef@1dfe813org.highwire.dtl.DTLVardef@fd5b3b_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗